GH4169 alloy, a nickel-based superalloy known for its excellent high temperature resistance, corrosion resistance, mechanical properties, and high-temperature tribological properties, is widely used in industrial applications, such as in gas turbines for space shuttles and rocket engines. This study addresses the issue of electrolyte product residue in the electrochemical machining process of a GH4169 alloy by utilizing a C6H5Na3O7-containing NaNO3 new mixed electrolyte. Comparative investigations of the electrochemical behavior and electrolyte product removal mechanisms at different concentrations of C6H5Na3O7 additive in NaNO3 solutions were conducted. The effects of additives, applied voltage, and the rotating speed of the cathode tool on the processing performance of micro-pit arrays on a GH4169 alloy were analyzed. The results indicate that the mixed solution containing C6H5Na3O7 significantly improves the localization and geometric morphology of the micro-pits compared to a single NaNO3 solution. The optimal electrochemical machining parameters were identified as 0.5 wt% C6H5Na3O7 + 10 wt% NaNO3 mixed electrolyte, 12 V applied voltage, and 0.1 r/min rotating speed of the cathode tool. Under these conditions, high-quality micro-pit arrays with an average diameter of 405.85 μm, an average depth of 87.5 μm, and an etch factor (EF) of 1.67 were successfully fabricated, exhibiting excellent morphology, localization, and consistency.